8FHB | pdb_00008fhb

Protein 32 with aldehyde deformylating oxidase activity from Synechococcus sp.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	298	30% PEG 4,000, 200 mM MgCl2, 100 mM HEPES HCl

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.192	α = 90
b = 74.33	β = 90
c = 111.953	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	298	PIXEL	DECTRIS PILATUS 6M		2022-05-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.979460	SSRL	BL9-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.95	37.32	100	0.059	0.061	0.017	1	26.7	13.2		17168			27.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	2	100		0.666	0.692	0.186	0.937	4.3	13.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	FREE R-VALUE	1.95	37.165	17143	826	99.901	0.172	0.1692	0.18	0.2167	0.22	0.05	35.558

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
0.004			0.018		-0.022

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.068
r_dihedral_angle_3_deg	15.201
r_dihedral_angle_2_deg	10.147
r_lrange_it	8.901
r_lrange_other	8.894
r_scangle_it	7.761
r_scangle_other	7.758
r_dihedral_angle_1_deg	6.013
r_scbond_it	5.778
r_scbond_other	5.774
r_mcangle_it	5.571
r_mcangle_other	5.569
r_mcbond_it	4.29
r_mcbond_other	4.288
r_angle_refined_deg	2.117
r_angle_other_deg	0.727
r_nbd_refined	0.234
r_symmetry_nbd_refined	0.226
r_symmetry_nbd_other	0.189
r_nbtor_refined	0.182
r_nbd_other	0.181
r_xyhbond_nbd_refined	0.169
r_symmetry_xyhbond_nbd_refined	0.141
r_chiral_restr	0.111
r_symmetry_nbtor_other	0.081
r_bond_refined_d	0.015
r_gen_planes_refined	0.014
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1614
Nucleic Acid Atoms
Solvent Atoms	85
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
REFMAC	phasing